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GeneBe

BCL7A

BAF chromatin remodeling complex subunit BCL7A, the group of BAF complex

Basic information

Region (hg38): 12:122019421-122062044

Previous symbols: [ "BCL7" ]

Links

ENSG00000110987NCBI:605OMIM:601406HGNC:1004Uniprot:Q4VC05AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BCL7A gene.

  • Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BCL7A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
7
clinvar
7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 7 0 0

Variants in BCL7A

This is a list of pathogenic ClinVar variants found in the BCL7A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
12-122043960-G-A not specified Uncertain significance (Aug 15, 2023)2590826
12-122044006-A-G not specified Uncertain significance (Nov 15, 2021)2370954
12-122044033-A-G not specified Uncertain significance (Jul 12, 2023)2610808
12-122054853-A-G not specified Uncertain significance (Sep 30, 2021)2252778
12-122054883-C-G BCL7A-related condition Likely benign (Jun 05, 2023)3045177
12-122054933-C-G not specified Uncertain significance (Nov 15, 2021)2261561
12-122054967-G-A not specified Uncertain significance (Apr 27, 2023)2541427
12-122054976-T-C not specified Uncertain significance (Nov 03, 2022)2374634

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BCL7Aprotein_codingprotein_codingENST00000538010 642621
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.07820.912125718071257250.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8981131430.7890.000008331519
Missense in Polyphen3150.6150.61246594
Synonymous-0.1326058.71.020.00000422434
Loss of Function2.25412.60.3177.34e-7131

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001160.000116
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.000008820.00000879
Middle Eastern0.0001090.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Disease
DISEASE: Note=Chromosomal aberrations involving BCL7A may be a cause of B-cell non-Hodgkin lymphoma. Three-way translocation t(8;14;12)(q24.1;q32.3;q24.1) with MYC and with immunoglobulin gene regions. {ECO:0000269|PubMed:8605326}.;
Pathway
TNFalpha (Consensus)

Recessive Scores

pRec
0.128

Intolerance Scores

loftool
0.379
rvis_EVS
0.08
rvis_percentile_EVS
60.09

Haploinsufficiency Scores

pHI
0.121
hipred
Y
hipred_score
0.640
ghis
0.461

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.405

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bcl7a
Phenotype
integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process
negative regulation of transcription, DNA-templated
Cellular component
cellular_component
Molecular function
molecular_function;protein binding